Variant report

Variant	rs2517612
Chromosome Location	chr6:30169092-30169093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30168209..30170458-chr6:30175226..30176879,2	MCF-7	breast:
2	chr6:30164991..30167307-chr6:30168742..30170547,2	K562	blood:
3	chr6:30168637..30170794-chr6:30170971..30172497,2	K562	blood:
4	chr6:30164021..30166889-chr6:30166891..30170637,4	MCF-7	breast:
5	chr6:30168287..30170293-chr6:30179032..30181257,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs2188100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2517613	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517615	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517618	0.93[EUR][1000 genomes]
rs2523715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523719	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2523720	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2844770	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2844771	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2844772	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2844773	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2844785	0.88[EUR][1000 genomes]
rs3094070	0.80[EUR][1000 genomes]
rs3094071	0.80[EUR][1000 genomes]
rs3094072	0.80[EUR][1000 genomes]
rs3094073	0.80[EUR][1000 genomes]
rs3094074	0.80[EUR][1000 genomes]
rs3094077	0.80[EUR][1000 genomes]
rs3094629	0.80[EUR][1000 genomes]
rs3094630	0.80[EUR][1000 genomes]
rs3094632	0.80[EUR][1000 genomes]
rs3129697	0.80[EUR][1000 genomes]
rs3129699	0.80[EUR][1000 genomes]
rs3129700	0.80[EUR][1000 genomes]
rs3129701	0.80[EUR][1000 genomes]
rs3129702	0.80[EUR][1000 genomes]
rs3129703	0.80[EUR][1000 genomes]
rs3129705	0.80[EUR][1000 genomes]
rs3129706	0.82[EUR][1000 genomes]
rs3129707	0.80[EUR][1000 genomes]
rs3129835	0.82[EUR][1000 genomes]
rs3129836	0.82[EUR][1000 genomes]
rs3130398	0.80[EUR][1000 genomes]
rs3130400	0.80[EUR][1000 genomes]
rs3130401	0.80[EUR][1000 genomes]
rs3130403	0.80[EUR][1000 genomes]
rs3130404	0.80[EUR][1000 genomes]
rs3130405	0.80[EUR][1000 genomes]
rs3132655	0.80[EUR][1000 genomes]
rs3132656	0.80[EUR][1000 genomes]
rs3132657	0.80[EUR][1000 genomes]
rs3132658	0.80[EUR][1000 genomes]
rs3132659	0.80[EUR][1000 genomes]
rs885913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885916	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9261629	0.80[EUR][1000 genomes]
rs9261630	0.80[EUR][1000 genomes]
rs929157	0.88[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2517612	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2517612	ZNF192	cis	parietal	SCAN
rs2517612	BTN2A1	cis	parietal	SCAN
rs2517612	ZKSCAN3	cis	parietal	SCAN
rs2517612	ZNF323	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30145000-30173800	Weak transcription	Right Atrium	heart
2	chr6:30148000-30173000	Weak transcription	Fetal Heart	heart
3	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:30151800-30170400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:30153200-30169800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
11	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
12	chr6:30161400-30169200	Strong transcription	Placenta	Placenta
13	chr6:30162400-30169200	Strong transcription	Fetal Stomach	stomach
14	chr6:30162400-30169400	Strong transcription	Colon Smooth Muscle	Colon
15	chr6:30162600-30170600	Strong transcription	Dnd41	blood
16	chr6:30162800-30169400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:30162800-30169400	Strong transcription	Primary T cells from cord blood	blood
18	chr6:30162800-30169400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:30162800-30170600	Strong transcription	Fetal Thymus	thymus
20	chr6:30163400-30169200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:30163800-30170600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:30164600-30169200	Strong transcription	Osteobl	bone
23	chr6:30166200-30170000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:30166400-30169600	Weak transcription	Stomach Mucosa	stomach
25	chr6:30166600-30169400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:30166600-30169400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:30167000-30173000	Weak transcription	Brain Germinal Matrix	brain
28	chr6:30167000-30178000	Weak transcription	Fetal Brain Female	brain
29	chr6:30167400-30169800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:30167800-30170400	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr6:30168000-30170000	Genic enhancers	Fetal Intestine Large	intestine
32	chr6:30168000-30170400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:30168000-30170400	Genic enhancers	HepG2	liver
34	chr6:30168200-30169200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:30168200-30169200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:30168200-30169200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:30168200-30169600	Strong transcription	A549	lung
38	chr6:30168200-30170000	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr6:30168200-30170000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:30168200-30170400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:30168200-30171200	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr6:30168400-30169200	Genic enhancers	Rectal Mucosa Donor 31	rectum
43	chr6:30168400-30169600	Weak transcription	HSMMtube	muscle
44	chr6:30168400-30170400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr6:30168400-30170600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
46	chr6:30168400-30174000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:30168600-30169400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:30168600-30170400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:30168600-30171200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:30168600-30171600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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